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lh3
bwa
C2020–2022
lh3 / bwa

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Science & Engineering
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4Distinct people
4Mentions
0Explicit recommenders
1.8KGitHub stars
REPOSITORY AT A GLANCE

What to know before exploring

What it is

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

GitHub

Where it is used

No documented product use has been verified yet.

What people are saying

No recommendation phrase was found in the indexed comments.

No classified warning is attached to this page. Read the discussions before treating silence as approval.

Also in these discussions

No other repository is repeatedly linked in the same discussions.

This week on Hacker News

Nov 7–Nov 14 UTC · Direct repository links and separately labeled related project stories. Indexed through 11/14/2026, 5:04:57 PM UTC.

No direct repository links were found in the indexed HN discussions over the past seven days. Older discussions are available below.

Mentions over time

HN mentions by month4 dated mentions

Observed mentions: 2020-05-19 14:28:31 UTC to 2022-10-11 02:04:26 UTC.

012020-05-01 00:00:00 UTC to 2020-06-01 00:00:00 UTC (exclusive): 1 mentions; 0 submissions, 1 commentsMay 20202020-06-01 00:00:00 UTC to 2020-07-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2020-07-01 00:00:00 UTC to 2020-08-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2020-08-01 00:00:00 UTC to 2020-09-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2020-09-01 00:00:00 UTC to 2020-10-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2020-10-01 00:00:00 UTC to 2020-11-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2020-11-01 00:00:00 UTC to 2020-12-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2020-12-01 00:00:00 UTC to 2021-01-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2021-01-01 00:00:00 UTC to 2021-02-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2021-02-01 00:00:00 UTC to 2021-03-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2021-03-01 00:00:00 UTC to 2021-04-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2021-04-01 00:00:00 UTC to 2021-05-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2021-05-01 00:00:00 UTC to 2021-06-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2021-06-01 00:00:00 UTC to 2021-07-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2021-07-01 00:00:00 UTC to 2021-08-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 commentsJul 20212021-08-01 00:00:00 UTC to 2021-09-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2021-09-01 00:00:00 UTC to 2021-10-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2021-10-01 00:00:00 UTC to 2021-11-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2021-11-01 00:00:00 UTC to 2021-12-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2021-12-01 00:00:00 UTC to 2022-01-01 00:00:00 UTC (exclusive): 1 mentions; 0 submissions, 1 comments2022-01-01 00:00:00 UTC to 2022-02-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2022-02-01 00:00:00 UTC to 2022-03-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2022-03-01 00:00:00 UTC to 2022-04-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2022-04-01 00:00:00 UTC to 2022-05-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2022-05-01 00:00:00 UTC to 2022-06-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2022-06-01 00:00:00 UTC to 2022-07-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2022-07-01 00:00:00 UTC to 2022-08-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2022-08-01 00:00:00 UTC to 2022-09-01 00:00:00 UTC (exclusive): 0 mentions; 0 submissions, 0 comments2022-09-01 00:00:00 UTC to 2022-10-01 00:00:00 UTC (exclusive): 1 mentions; 0 submissions, 1 comments2022-10-01 00:00:00 UTC to 2022-11-01 00:00:00 UTC (exclusive): 1 mentions; 0 submissions, 1 commentsOct 2022

Counts come from the repository’s dated source evidence. Index cutoff: 2026-11-02 08:16:59 UTC.

View mention counts and date ranges
UTC ranges include their start and exclude their end. Select a period to filter the source evidence.
PeriodStart (UTC)End (exclusive, UTC)MentionsSubmissionsComments
May 20202020-05-01 00:00:00 UTC2020-06-01 00:00:00 UTC101
Jun 20202020-06-01 00:00:00 UTC2020-07-01 00:00:00 UTC000
Jul 20202020-07-01 00:00:00 UTC2020-08-01 00:00:00 UTC000
Aug 20202020-08-01 00:00:00 UTC2020-09-01 00:00:00 UTC000
Sep 20202020-09-01 00:00:00 UTC2020-10-01 00:00:00 UTC000
Oct 20202020-10-01 00:00:00 UTC2020-11-01 00:00:00 UTC000
Nov 20202020-11-01 00:00:00 UTC2020-12-01 00:00:00 UTC000
Dec 20202020-12-01 00:00:00 UTC2021-01-01 00:00:00 UTC000
Jan 20212021-01-01 00:00:00 UTC2021-02-01 00:00:00 UTC000
Feb 20212021-02-01 00:00:00 UTC2021-03-01 00:00:00 UTC000
Mar 20212021-03-01 00:00:00 UTC2021-04-01 00:00:00 UTC000
Apr 20212021-04-01 00:00:00 UTC2021-05-01 00:00:00 UTC000
May 20212021-05-01 00:00:00 UTC2021-06-01 00:00:00 UTC000
Jun 20212021-06-01 00:00:00 UTC2021-07-01 00:00:00 UTC000
Jul 20212021-07-01 00:00:00 UTC2021-08-01 00:00:00 UTC000
Aug 20212021-08-01 00:00:00 UTC2021-09-01 00:00:00 UTC000
Sep 20212021-09-01 00:00:00 UTC2021-10-01 00:00:00 UTC000
Oct 20212021-10-01 00:00:00 UTC2021-11-01 00:00:00 UTC000
Nov 20212021-11-01 00:00:00 UTC2021-12-01 00:00:00 UTC000
Dec 20212021-12-01 00:00:00 UTC2022-01-01 00:00:00 UTC101
Jan 20222022-01-01 00:00:00 UTC2022-02-01 00:00:00 UTC000
Feb 20222022-02-01 00:00:00 UTC2022-03-01 00:00:00 UTC000
Mar 20222022-03-01 00:00:00 UTC2022-04-01 00:00:00 UTC000
Apr 20222022-04-01 00:00:00 UTC2022-05-01 00:00:00 UTC000
May 20222022-05-01 00:00:00 UTC2022-06-01 00:00:00 UTC000
Jun 20222022-06-01 00:00:00 UTC2022-07-01 00:00:00 UTC000
Jul 20222022-07-01 00:00:00 UTC2022-08-01 00:00:00 UTC000
Aug 20222022-08-01 00:00:00 UTC2022-09-01 00:00:00 UTC000
Sep 20222022-09-01 00:00:00 UTC2022-10-01 00:00:00 UTC101
Oct 20222022-10-01 00:00:00 UTC2022-11-01 00:00:00 UTC101

What Hacker News says

4 sources
aaauaucuggaa·Oct 11, 2022
Start with downloading SRA toolkit: https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-To... Find some data of interest: https://www.ncbi.nlm.nih.gov/sra?term=(%22Homo%20sapiens%22[... (This searches SRA for human genome sequences on illumina with fastq files available) Run fasterq-dump on the SRR (listed as "Runs" in the SRA page of your choice): fasterq-dump SRR21812682 Download a microbial genome of interest, here is the link for common yeast: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF... Install an alignment tool like bwa: https://github.com/lh3/bwa Unzip the the genome file and create a bwa index: gunzip GCF_000146045.2_R64_genomic.fna.gz && bwa index GCF_000146045.2_R64_genomic.fna Align: bwa GCF_000146045.2_R64_genomic.fna SRR21812682.fastq (or whatever the fastq files are named) If you get any alignment re
Read the rest
sults, you've "found" fungal DNA in a human sample. This is a highly simplified workflow, but covers the basic ideas. One of the papers is free and the method sections covers their workflow (it is much more complicated): https://www.cell.com/cell/fulltext/S0092-8674(22)01127-8 Useful resources: https://www.biostars.org/ https://rosalind.info/problems/list-view/?location=bioinform... https://www.cancer.gov/about-nci/organization/ccg/research/s... (source data for this paper, cancer specific sequencing data)
In Scientists are finding fungi in cancerous tumors
teekert·Dec 8, 2021
Aligning all the short reads a (Sequencing By Synthesis) Next Generation Sequencer (to be very specific) produces (hundreds to thousands of millions) to a reference genome is hard computational work indeed, no idea if you can use it for proof-of-work but I like where this is going... But do you not need some kind of definition of correct (like hash needs many leading 0's) for PoW? How would that work for aligning reads to a reference genome? Maybe it could, find the position of the read is hard (I mean, not really for a modern CPU but relatively... I think... not an expert on that), verifying how correct it is, is not hard (I think). Maybe we should ask the BWA devs [0]. [0]: https://github.com/lh3/bwa
In RNA Takes Over

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